NPASS Compound

Structure

CID19841 OpenBabel06191715342D 23 23 0 0 1 0 0 0 0 0999 V2000 9.5916 4.2644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5691 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1848 5.1780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1903 5.2825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6025 4.4735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6080 4.5780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0202 3.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0257 3.8735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4379 3.0645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4434 3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8556 2.3600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8611 2.4646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2733 1.6555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2788 1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6180 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 0.9511 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3090 0.9511 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8968 1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -0.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4901 2.6736 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8913 1.6555 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -1.5878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 2 15 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 15 17 1 0 0 0 0 15 19 1 0 0 0 0 16 14 1 6 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 1 0 0 0 18 20 2 0 0 0 0 18 21 1 0 0 0 0 19 22 2 0 0 0 0 19 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	324.23
Volume:	355.875
LogP:	6.725
LogD:	4.579
LogS:	-3.641
# Rotatable Bonds:	13
TPSA:	70.67
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.447
Synthetic Accessibility Score:	2.542
Fsp3:	0.737
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.08
MDCK Permeability:	3.0093533496255986e-05
Pgp-inhibitor:	0.013
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.232
30% Bioavailability (F30%):	0.862

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.129
Plasma Protein Binding (PPB):	100.2530288696289%
Volume Distribution (VD):	0.867
Pgp-substrate:	1.5804837942123413%

ADMET: Metabolism

CYP1A2-inhibitor:	0.235
CYP1A2-substrate:	0.196
CYP2C19-inhibitor:	0.118
CYP2C19-substrate:	0.068
CYP2C9-inhibitor:	0.249
CYP2C9-substrate:	0.672
CYP2D6-inhibitor:	0.086
CYP2D6-substrate:	0.092
CYP3A4-inhibitor:	0.031
CYP3A4-substrate:	0.017

ADMET: Excretion

Clearance (CL):	2.262
Half-life (T1/2):	0.437

ADMET: Toxicity

hERG Blockers:	0.01
Human Hepatotoxicity (H-HT):	0.438
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.109
Maximum Recommended Daily Dose:	0.013
Skin Sensitization:	0.84
Carcinogencity:	0.064
Eye Corrosion:	0.041
Eye Irritation:	0.654
Respiratory Toxicity:	0.919

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC19841

Natural Product ID:	NPC19841
*Common Name:**	Protolichesterinic Acid
IUPAC Name:	(2S,3R)-4-methylidene-5-oxo-2-tridecyloxolane-3-carboxylic acid
Synonyms:	(+)-Protolichesterinic Acid; Protolichesterinic Acid
Standard InCHIKey:	WZYZDHVPSZCEEP-DLBZAZTESA-N
Standard InCHI:	InChI=1S/C19H32O4/c1-3-4-5-6-7-8-9-10-11-12-13-14-16-17(18(20)21)15(2)19(22)23-16/h16-17H,2-14H2,1H3,(H,20,21)/t16-,17+/m0/s1
SMILES:	CCCCCCCCCCCCC[C@H]1[C@@H](C(=C)C(=O)O1)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL490329
PubChem CID:	468953
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[22233034]
NPO3729	Cetraria islandica	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561895]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25424	Putterlickia verrucosa	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6513	Vernonia condensata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3729	Cetraria islandica	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4633	Calypogeia integristipula	Species	Calypogeiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2777	Cirsium brevistylum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5786	Desmodium oxyphyllum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25424	Putterlickia verrucosa	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
ED50	4
IC50	9
Ki	2
Others	6

Activity Type	# Activity
Cell Line	6
Individual Protein	7
NON-MOLECULAR	1
Others	6
Uncleic Acid	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	IC50	=	24300.0	nM	PMID[461296]
NPT59	Individual Protein	DNA polymerase beta	Homo sapiens	IC50	=	7400.0	nM	PMID[461296]
NPT91	Cell Line	KB	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[461296]
NPT1034	Cell Line	Lu1	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[461296]
NPT858	Cell Line	LNCaP	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[461296]
NPT133	Cell Line	ZR-75-1	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[461296]
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	Inhibition	=	99.0	%	PMID[461296]
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	Inhibition	=	52.0	%	PMID[461296]
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	Inhibition	=	19.0	%	PMID[461296]
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	Ki	=	10000.0	nM	PMID[461296]
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	Ki	=	7100.0	nM	PMID[461296]
NPT1195	Cell Line	PMNL		IC50	=	9000.0	nM	PMID[461297]
NPT941	Cell Line	HaCaT	Homo sapiens	IC50	>	5000.0	nM	PMID[461298]
NPT2	Others	Unspecified		IC50	=	29600.0	nM	PMID[461296]
NPT2	Others	Unspecified		IC50	=	21900.0	nM	PMID[461296]
NPT2	Others	Unspecified		IC50	=	92800.0	nM	PMID[461296]
NPT1514	Uncleic Acid	DNA	Bos taurus	Inhibition	=	1.3	%	PMID[461296]
NPT2	Others	Unspecified		IC50	>	200000.0	nM	PMID[461297]
NPT2	Others	Unspecified		Activity	=	0.08	umol	PMID[461297]
NPT1	Others	Radical scavenging activity		Activity	<	1.0	/M/s	PMID[461297]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	8600.0	nM	PMID[461299]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC19841 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	184
0.1-0.2	1483
0.2-0.3	5976
0.3-0.4	14676
0.4-0.5	10207
0.5-0.6	6740
0.6-0.7	2622
0.7-0.8	720
0.8-0.85	81
0.85-0.9	6
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9315	High Similarity	NPC48641
0.8434	Intermediate Similarity	NPC469483
0.8415	Intermediate Similarity	NPC158756
0.8313	Intermediate Similarity	NPC470755
0.8313	Intermediate Similarity	NPC255307
0.8256	Intermediate Similarity	NPC19087
0.8235	Intermediate Similarity	NPC476803
0.8235	Intermediate Similarity	NPC476805
0.8228	Intermediate Similarity	NPC97516
0.8228	Intermediate Similarity	NPC122847
0.8214	Intermediate Similarity	NPC162071
0.8214	Intermediate Similarity	NPC475461
0.8214	Intermediate Similarity	NPC469910
0.8214	Intermediate Similarity	NPC305475
0.8214	Intermediate Similarity	NPC150755
0.8193	Intermediate Similarity	NPC96259
0.8193	Intermediate Similarity	NPC476804
0.8193	Intermediate Similarity	NPC114979
0.8193	Intermediate Similarity	NPC141193
0.8193	Intermediate Similarity	NPC191476
0.8161	Intermediate Similarity	NPC184063
0.814	Intermediate Similarity	NPC38392
0.814	Intermediate Similarity	NPC12872
0.814	Intermediate Similarity	NPC168679
0.8125	Intermediate Similarity	NPC108816
0.8125	Intermediate Similarity	NPC93763
0.8118	Intermediate Similarity	NPC201658
0.8095	Intermediate Similarity	NPC165162
0.809	Intermediate Similarity	NPC475900
0.8077	Intermediate Similarity	NPC140287
0.8072	Intermediate Similarity	NPC169575
0.8072	Intermediate Similarity	NPC131669
0.8072	Intermediate Similarity	NPC473390
0.8072	Intermediate Similarity	NPC475947
0.8072	Intermediate Similarity	NPC40746
0.8068	Intermediate Similarity	NPC469645
0.8068	Intermediate Similarity	NPC469692
0.8068	Intermediate Similarity	NPC475302
0.8049	Intermediate Similarity	NPC25684
0.8049	Intermediate Similarity	NPC24417
0.8049	Intermediate Similarity	NPC301477
0.8049	Intermediate Similarity	NPC141810
0.8049	Intermediate Similarity	NPC471325
0.8049	Intermediate Similarity	NPC281949
0.8025	Intermediate Similarity	NPC470244
0.8025	Intermediate Similarity	NPC167881
0.8025	Intermediate Similarity	NPC617
0.8025	Intermediate Similarity	NPC470239
0.8025	Intermediate Similarity	NPC98557
0.8023	Intermediate Similarity	NPC177629
0.8023	Intermediate Similarity	NPC217983
0.8023	Intermediate Similarity	NPC58219
0.8023	Intermediate Similarity	NPC477302
0.8023	Intermediate Similarity	NPC475819
0.8023	Intermediate Similarity	NPC207114
0.8	Intermediate Similarity	NPC470240
0.8	Intermediate Similarity	NPC116177
0.8	Intermediate Similarity	NPC261721
0.8	Intermediate Similarity	NPC171204
0.8	Intermediate Similarity	NPC304558
0.8	Intermediate Similarity	NPC39859
0.8	Intermediate Similarity	NPC238593
0.8	Intermediate Similarity	NPC476028
0.8	Intermediate Similarity	NPC141789
0.8	Intermediate Similarity	NPC158416
0.8	Intermediate Similarity	NPC470883
0.8	Intermediate Similarity	NPC236692
0.8	Intermediate Similarity	NPC320630
0.8	Intermediate Similarity	NPC476794
0.8	Intermediate Similarity	NPC7563
0.8	Intermediate Similarity	NPC76862
0.8	Intermediate Similarity	NPC309757
0.7978	Intermediate Similarity	NPC121825
0.7955	Intermediate Similarity	NPC184463
0.7952	Intermediate Similarity	NPC229825
0.7952	Intermediate Similarity	NPC89555
0.7931	Intermediate Similarity	NPC92974
0.7931	Intermediate Similarity	NPC218927
0.7931	Intermediate Similarity	NPC206001
0.7931	Intermediate Similarity	NPC307411
0.7927	Intermediate Similarity	NPC223904
0.7907	Intermediate Similarity	NPC186148
0.7901	Intermediate Similarity	NPC267231
0.7889	Intermediate Similarity	NPC475659
0.7882	Intermediate Similarity	NPC149725
0.7882	Intermediate Similarity	NPC47958
0.7882	Intermediate Similarity	NPC304509
0.7865	Intermediate Similarity	NPC473273
0.7865	Intermediate Similarity	NPC473263
0.7865	Intermediate Similarity	NPC476300
0.7865	Intermediate Similarity	NPC308656
0.7865	Intermediate Similarity	NPC60386
0.7865	Intermediate Similarity	NPC473234
0.7857	Intermediate Similarity	NPC245665
0.7857	Intermediate Similarity	NPC59097
0.7857	Intermediate Similarity	NPC128429
0.7857	Intermediate Similarity	NPC318468
0.7848	Intermediate Similarity	NPC476355
0.7841	Intermediate Similarity	NPC474232
0.7841	Intermediate Similarity	NPC206614
0.7841	Intermediate Similarity	NPC51004
0.7841	Intermediate Similarity	NPC297474
0.7841	Intermediate Similarity	NPC54065
0.7841	Intermediate Similarity	NPC469368
0.7841	Intermediate Similarity	NPC474323
0.7838	Intermediate Similarity	NPC53642
0.7838	Intermediate Similarity	NPC470325
0.7831	Intermediate Similarity	NPC52861
0.7821	Intermediate Similarity	NPC163003
0.7821	Intermediate Similarity	NPC474590
0.7816	Intermediate Similarity	NPC202672
0.7816	Intermediate Similarity	NPC136879
0.7816	Intermediate Similarity	NPC79549
0.7805	Intermediate Similarity	NPC270126
0.7805	Intermediate Similarity	NPC178277
0.7802	Intermediate Similarity	NPC142529
0.7802	Intermediate Similarity	NPC476009
0.7802	Intermediate Similarity	NPC473859
0.7802	Intermediate Similarity	NPC230800
0.7802	Intermediate Similarity	NPC91771
0.7791	Intermediate Similarity	NPC187661
0.7791	Intermediate Similarity	NPC474949
0.7791	Intermediate Similarity	NPC475019
0.7791	Intermediate Similarity	NPC476015
0.7791	Intermediate Similarity	NPC474762
0.7791	Intermediate Similarity	NPC470242
0.7778	Intermediate Similarity	NPC474760
0.7765	Intermediate Similarity	NPC474780
0.7765	Intermediate Similarity	NPC156485
0.7765	Intermediate Similarity	NPC115786
0.7765	Intermediate Similarity	NPC159635
0.7753	Intermediate Similarity	NPC261607
0.7753	Intermediate Similarity	NPC29821
0.7753	Intermediate Similarity	NPC300312
0.7753	Intermediate Similarity	NPC63193
0.7753	Intermediate Similarity	NPC293001
0.7753	Intermediate Similarity	NPC57304
0.7753	Intermediate Similarity	NPC111114
0.7753	Intermediate Similarity	NPC171360
0.7753	Intermediate Similarity	NPC133888
0.7753	Intermediate Similarity	NPC35959
0.7753	Intermediate Similarity	NPC30515
0.7753	Intermediate Similarity	NPC133698
0.775	Intermediate Similarity	NPC155587
0.775	Intermediate Similarity	NPC193351
0.775	Intermediate Similarity	NPC226669
0.775	Intermediate Similarity	NPC138408
0.7738	Intermediate Similarity	NPC246076
0.7727	Intermediate Similarity	NPC155935
0.7727	Intermediate Similarity	NPC215556
0.7717	Intermediate Similarity	NPC474313
0.7717	Intermediate Similarity	NPC169205
0.7711	Intermediate Similarity	NPC6823
0.7711	Intermediate Similarity	NPC281132
0.7701	Intermediate Similarity	NPC190753
0.7701	Intermediate Similarity	NPC72513
0.7701	Intermediate Similarity	NPC5130
0.7701	Intermediate Similarity	NPC118601
0.7692	Intermediate Similarity	NPC90121
0.7692	Intermediate Similarity	NPC193645
0.7692	Intermediate Similarity	NPC275960
0.7692	Intermediate Similarity	NPC36954
0.7692	Intermediate Similarity	NPC48803
0.7683	Intermediate Similarity	NPC471465
0.7683	Intermediate Similarity	NPC218817
0.7683	Intermediate Similarity	NPC11796
0.7683	Intermediate Similarity	NPC128276
0.7683	Intermediate Similarity	NPC196653
0.7674	Intermediate Similarity	NPC329749
0.7674	Intermediate Similarity	NPC125290
0.7667	Intermediate Similarity	NPC475838
0.7667	Intermediate Similarity	NPC153590
0.7667	Intermediate Similarity	NPC125674
0.7667	Intermediate Similarity	NPC475912
0.7667	Intermediate Similarity	NPC228451
0.7667	Intermediate Similarity	NPC212486
0.766	Intermediate Similarity	NPC110443
0.766	Intermediate Similarity	NPC185141
0.766	Intermediate Similarity	NPC128733
0.766	Intermediate Similarity	NPC46998
0.766	Intermediate Similarity	NPC133907
0.7654	Intermediate Similarity	NPC235906
0.7654	Intermediate Similarity	NPC123360
0.7647	Intermediate Similarity	NPC54468
0.7647	Intermediate Similarity	NPC250315
0.764	Intermediate Similarity	NPC129419
0.764	Intermediate Similarity	NPC71533
0.764	Intermediate Similarity	NPC216284
0.764	Intermediate Similarity	NPC475855
0.764	Intermediate Similarity	NPC179394
0.764	Intermediate Similarity	NPC144133
0.764	Intermediate Similarity	NPC106510
0.764	Intermediate Similarity	NPC35809
0.7634	Intermediate Similarity	NPC141191
0.7625	Intermediate Similarity	NPC320537
0.7625	Intermediate Similarity	NPC143979
0.7619	Intermediate Similarity	NPC79277
0.7619	Intermediate Similarity	NPC475481
0.7614	Intermediate Similarity	NPC178875
0.7609	Intermediate Similarity	NPC185553

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC19841 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	215
0.1-0.2	2225
0.2-0.3	3746
0.3-0.4	1997
0.4-0.5	632
0.5-0.6	274
0.6-0.7	49
0.7-0.8	12
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7692	Intermediate Similarity	NPD1698	Clinical (unspecified phase)
0.7444	Intermediate Similarity	NPD5785	Approved
0.7273	Intermediate Similarity	NPD7899	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD5363	Approved
0.7253	Intermediate Similarity	NPD6698	Approved
0.7253	Intermediate Similarity	NPD46	Approved
0.7241	Intermediate Similarity	NPD7154	Phase 3
0.7209	Intermediate Similarity	NPD5369	Approved
0.7191	Intermediate Similarity	NPD5786	Approved
0.7126	Intermediate Similarity	NPD4269	Approved
0.7126	Intermediate Similarity	NPD4270	Approved
0.7079	Intermediate Similarity	NPD1733	Clinical (unspecified phase)
0.6989	Remote Similarity	NPD7983	Approved
0.6957	Remote Similarity	NPD1695	Approved
0.6932	Remote Similarity	NPD6435	Approved
0.6907	Remote Similarity	NPD4225	Approved
0.6897	Remote Similarity	NPD4252	Approved
0.6897	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6893	Remote Similarity	NPD6371	Approved
0.6889	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.6854	Remote Similarity	NPD5362	Discontinued
0.6774	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD6101	Approved
0.6737	Remote Similarity	NPD5778	Approved
0.6737	Remote Similarity	NPD5779	Approved
0.6737	Remote Similarity	NPD6399	Phase 3
0.6705	Remote Similarity	NPD4820	Approved
0.6705	Remote Similarity	NPD4821	Approved
0.6705	Remote Similarity	NPD5368	Approved
0.6705	Remote Similarity	NPD4822	Approved
0.6705	Remote Similarity	NPD4819	Approved
0.6702	Remote Similarity	NPD7838	Discovery
0.6667	Remote Similarity	NPD5282	Discontinued
0.6667	Remote Similarity	NPD4271	Approved
0.6667	Remote Similarity	NPD4268	Approved
0.6632	Remote Similarity	NPD8035	Phase 2
0.6632	Remote Similarity	NPD8034	Phase 2
0.6632	Remote Similarity	NPD6411	Approved
0.6566	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6559	Remote Similarity	NPD4250	Approved
0.6559	Remote Similarity	NPD4251	Approved
0.6556	Remote Similarity	NPD5209	Approved
0.6556	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6531	Remote Similarity	NPD7839	Suspended
0.6522	Remote Similarity	NPD1694	Approved
0.6477	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6452	Remote Similarity	NPD4249	Approved
0.6421	Remote Similarity	NPD5370	Suspended
0.6381	Remote Similarity	NPD6686	Approved
0.6364	Remote Similarity	NPD7115	Discovery
0.6355	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.6322	Remote Similarity	NPD8039	Approved
0.6304	Remote Similarity	NPD5332	Approved
0.6304	Remote Similarity	NPD5331	Approved
0.63	Remote Similarity	NPD7902	Approved
0.6289	Remote Similarity	NPD4810	Clinical (unspecified phase)
0.6289	Remote Similarity	NPD7637	Suspended
0.6264	Remote Similarity	NPD4790	Discontinued
0.6237	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.622	Remote Similarity	NPD9496	Clinical (unspecified phase)
0.622	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6203	Remote Similarity	NPD3198	Approved
0.619	Remote Similarity	NPD229	Approved
0.6184	Remote Similarity	NPD3729	Clinical (unspecified phase)
0.6147	Remote Similarity	NPD6053	Discontinued
0.614	Remote Similarity	NPD8516	Approved
0.614	Remote Similarity	NPD8515	Approved
0.614	Remote Similarity	NPD8517	Approved
0.614	Remote Similarity	NPD8513	Phase 3
0.6111	Remote Similarity	NPD4238	Approved
0.6111	Remote Similarity	NPD4802	Phase 2
0.6105	Remote Similarity	NPD6422	Discontinued
0.6078	Remote Similarity	NPD7638	Approved
0.6075	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.6055	Remote Similarity	NPD6649	Approved
0.6055	Remote Similarity	NPD6650	Approved
0.6022	Remote Similarity	NPD4800	Clinical (unspecified phase)
0.6019	Remote Similarity	NPD7639	Approved
0.6019	Remote Similarity	NPD6373	Approved
0.6019	Remote Similarity	NPD7640	Approved
0.6019	Remote Similarity	NPD6372	Approved
0.6	Remote Similarity	NPD7900	Approved
0.6	Remote Similarity	NPD4756	Discovery
0.6	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.6	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6	Remote Similarity	NPD7748	Approved
0.598	Remote Similarity	NPD6083	Phase 2
0.598	Remote Similarity	NPD6084	Phase 2
0.5974	Remote Similarity	NPD3730	Approved
0.5974	Remote Similarity	NPD3728	Approved
0.5963	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.5962	Remote Similarity	NPD5344	Discontinued
0.5952	Remote Similarity	NPD7331	Phase 2
0.5941	Remote Similarity	NPD5695	Phase 3
0.5938	Remote Similarity	NPD7146	Approved
0.5938	Remote Similarity	NPD7521	Approved
0.5938	Remote Similarity	NPD6409	Approved
0.5938	Remote Similarity	NPD6684	Approved
0.5938	Remote Similarity	NPD5330	Approved
0.5938	Remote Similarity	NPD7334	Approved
0.5934	Remote Similarity	NPD3732	Approved
0.5926	Remote Similarity	NPD6881	Approved
0.5926	Remote Similarity	NPD6899	Approved
0.5922	Remote Similarity	NPD5696	Approved
0.5904	Remote Similarity	NPD3197	Phase 1
0.5904	Remote Similarity	NPD7909	Approved
0.5888	Remote Similarity	NPD5739	Approved
0.5888	Remote Similarity	NPD7128	Approved
0.5888	Remote Similarity	NPD6675	Approved
0.5888	Remote Similarity	NPD6402	Approved
0.5882	Remote Similarity	NPD8074	Phase 3
0.5865	Remote Similarity	NPD6648	Approved
0.5862	Remote Similarity	NPD8269	Approved
0.5862	Remote Similarity	NPD8267	Approved
0.5862	Remote Similarity	NPD8266	Approved
0.5862	Remote Similarity	NPD8268	Approved
0.5833	Remote Similarity	NPD5697	Approved
0.5833	Remote Similarity	NPD7341	Phase 2
0.5818	Remote Similarity	NPD7102	Approved
0.5818	Remote Similarity	NPD7290	Approved
0.5818	Remote Similarity	NPD6883	Approved
0.5816	Remote Similarity	NPD5737	Approved
0.5816	Remote Similarity	NPD6672	Approved
0.5816	Remote Similarity	NPD6903	Approved
0.5816	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.5804	Remote Similarity	NPD8133	Approved
0.58	Remote Similarity	NPD7515	Phase 2
0.5789	Remote Similarity	NPD4788	Approved
0.578	Remote Similarity	NPD7320	Approved
0.5769	Remote Similarity	NPD3196	Approved
0.5769	Remote Similarity	NPD3195	Phase 2
0.5769	Remote Similarity	NPD9298	Approved
0.5769	Remote Similarity	NPD3194	Approved
0.5769	Remote Similarity	NPD615	Clinical (unspecified phase)
0.5769	Remote Similarity	NPD4266	Approved
0.5766	Remote Similarity	NPD6869	Approved
0.5766	Remote Similarity	NPD6847	Approved
0.5766	Remote Similarity	NPD6617	Approved
0.5766	Remote Similarity	NPD8130	Phase 1
0.5763	Remote Similarity	NPD7830	Approved
0.5763	Remote Similarity	NPD7642	Approved
0.5763	Remote Similarity	NPD7829	Approved
0.5753	Remote Similarity	NPD634	Phase 3
0.5729	Remote Similarity	NPD4786	Approved
0.5727	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.5727	Remote Similarity	NPD6014	Approved
0.5727	Remote Similarity	NPD6013	Approved
0.5727	Remote Similarity	NPD6012	Approved
0.5714	Remote Similarity	NPD7966	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD3186	Phase 1
0.5714	Remote Similarity	NPD8297	Approved
0.5714	Remote Similarity	NPD6882	Approved
0.5688	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.5688	Remote Similarity	NPD5701	Approved
0.5684	Remote Similarity	NPD3667	Approved
0.5652	Remote Similarity	NPD7500	Approved
0.5644	Remote Similarity	NPD5281	Approved
0.5644	Remote Similarity	NPD5693	Phase 1
0.5644	Remote Similarity	NPD5284	Approved
0.5641	Remote Similarity	NPD3172	Approved
0.5638	Remote Similarity	NPD4695	Discontinued
0.5636	Remote Similarity	NPD6011	Approved
0.5631	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD2204	Approved
0.5616	Remote Similarity	NPD2699	Approved
0.5612	Remote Similarity	NPD3618	Phase 1
0.5612	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.5607	Remote Similarity	NPD7632	Discontinued
0.5603	Remote Similarity	NPD7641	Discontinued
0.56	Remote Similarity	NPD6125	Clinical (unspecified phase)
0.56	Remote Similarity	NPD622	Approved

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data